miRBooking-scan explore miRBooking

The miRBooking-scan Web service provides an exploratory view of reference microtargetomes computed by miRBooking.

Not interested in MCF-7? Choose a different cell line.

MCF-7

[...]

You're now looking into MCF-7 cell line. We need more detail such as:

  • link to a reference dataset (i.e. GEO)
  • miRBooking parameters used for the computation
  • initial quantifications

Here's how you can reproduce this:

mirbooking --targets=GCF_000001405.25_GRCh37.p13_rna.fna --mirnas=mature.fa --cds-regions=[...] --score-table=scores --log-base=512 --threshold=0.0179 --quantities=mcf7.tsv

Download this view:

curl -H Accept:text/tab-separated-values http://major.iric.ca/~poirigui/cgi-bin/mirbooking-scan/app.cgi/cell-lines/mcf7

target_accession position mirna_accession target_name target_quantity location vacancy mirna_name mirna_quantity probability occupancy silencing
NM_001402.5 10 MIMAT0000098 EEF1A1 9041.62 5'UTR 8385.62 hsa-miR-100-5p 536.929 0.018 168 0.31
NM_001402.5 10 MIMAT0000689 EEF1A1 9041.62 5'UTR 8385.62 hsa-miR-99b-5p 5044.02 0.018 228 0.42
NM_001402.5 10 MIMAT0000097 EEF1A1 9041.62 5'UTR 8385.62 hsa-miR-99a-5p 16757.0 0.018 260 0.479
NM_001402.5 130 MIMAT0004563 EEF1A1 9041.62 CDS 7869.62 hsa-miR-199b-3p 566.849 0.06 556 3.359
NM_001402.5 130 MIMAT0000232 EEF1A1 9041.62 CDS 7869.62 hsa-miR-199a-3p 1133.69 0.06 616 3.722
NM_001402.5 131 MIMAT0004569 EEF1A1 9041.62 CDS 7869.62 hsa-miR-222-5p 669.7 0.018 170 0.306
NM_001402.5 198 MIMAT0000461 EEF1A1 9041.62 CDS 7084.62 hsa-miR-195-5p 19353.9 0.019 269 0.509
NM_001402.5 198 MIMAT0000077 EEF1A1 9041.62 CDS 7084.62 hsa-miR-22-3p 21276.801 0.019 281 0.547
NM_001402.5 198 MIMAT0000417 EEF1A1 9041.62 CDS 7084.62 hsa-miR-15b-5p 22351.699 0.019 273 0.516
NM_001402.5 198 MIMAT0002820 EEF1A1 9041.62 CDS 7084.62 hsa-miR-497-5p 22387.4 0.019 274 0.518
NM_001402.5 198 MIMAT0000068 EEF1A1 9041.62 CDS 7084.62 hsa-miR-15a-5p 22496.699 0.019 274 0.518
NM_001402.5 198 MIMAT0001341 EEF1A1 9041.62 CDS 7084.62 hsa-miR-424-5p 22657.4 0.019 274 0.518
NM_001402.5 198 MIMAT0000069 EEF1A1 9041.62 CDS 7084.62 hsa-miR-16-5p 87584.602 0.019 312 0.59
NM_001402.5 217 MIMAT0004926 EEF1A1 9041.62 CDS 7084.62 hsa-miR-708-5p 8435.37 0.031 407 1.261
NM_001402.5 217 MIMAT0000085 EEF1A1 9041.62 CDS 7084.62 hsa-miR-28-5p 16043.8 0.031 435 1.348
NM_001402.5 249 MIMAT0000088 EEF1A1 9041.62 CDS 7714.62 hsa-miR-30a-3p 1853.87 0.052 570 2.974
NM_001402.5 249 MIMAT0000693 EEF1A1 9041.62 CDS 7714.62 hsa-miR-30e-3p 21986.699 0.052 757 3.95
NM_001402.5 288 MIMAT0010214 EEF1A1 9041.62 CDS 8575.62 hsa-miR-151b 2571.18 0.018 204 0.369
NM_001402.5 288 MIMAT0004697 EEF1A1 9041.62 CDS 8575.62 hsa-miR-151a-5p 21898.801 0.018 262 0.474
NM_001402.5 411 MIMAT0002874 EEF1A1 9041.62 CDS 1120.62 hsa-miR-503-5p 8657.98 0.027 348 0.94
NM_001402.5 411 MIMAT0000461 EEF1A1 9041.62 CDS 1120.62 hsa-miR-195-5p 19353.9 0.085 1219 10.382
NM_001402.5 411 MIMAT0000417 EEF1A1 9041.62 CDS 1120.62 hsa-miR-15b-5p 22351.699 0.085 1237 10.535
NM_001402.5 411 MIMAT0002820 EEF1A1 9041.62 CDS 1120.62 hsa-miR-497-5p 22387.4 0.085 1237 10.535
NM_001402.5 411 MIMAT0000068 EEF1A1 9041.62 CDS 1120.62 hsa-miR-15a-5p 22496.699 0.085 1237 10.535
NM_001402.5 411 MIMAT0001341 EEF1A1 9041.62 CDS 1120.62 hsa-miR-424-5p 22657.4 0.085 1238 10.544
NM_001402.5 411 MIMAT0000069 EEF1A1 9041.62 CDS 1120.62 hsa-miR-16-5p 87584.602 0.085 1405 11.966
NM_001402.5 417 MIMAT0000681 EEF1A1 9041.62 CDS 1120.62 hsa-miR-29c-3p 2401.56 0.019 211 0.394
NM_001402.5 417 MIMAT0000086 EEF1A1 9041.62 CDS 1120.62 hsa-miR-29a-3p 3949.07 0.019 225 0.42
NM_001402.5 417 MIMAT0000100 EEF1A1 9041.62 CDS 1120.62 hsa-miR-29b-3p 8998.69 0.019 247 0.461
NM_001402.5 417 MIMAT0004494 EEF1A1 9041.62 CDS 1120.62 hsa-miR-21-3p 22142.9 0.043 629 2.726
NM_001402.5 536 MIMAT0000080 EEF1A1 9041.62 CDS 7484.62 hsa-miR-24-3p 23929.5 0.107 1557 16.585
NM_001402.5 583 MIMAT0004809 EEF1A1 9041.62 CDS 7758.62 hsa-miR-628-5p 564.429 0.082 564 4.618
NM_001402.5 587 MIMAT0000103 EEF1A1 9041.62 CDS 7758.62 hsa-miR-106a-5p 3055.2 0.018 213 0.389
NM_001402.5 587 MIMAT0000070 EEF1A1 9041.62 CDS 7758.62 hsa-miR-17-5p 22117.0 0.018 265 0.484
NM_001402.5 587 MIMAT0000075 EEF1A1 9041.62 CDS 7758.62 hsa-miR-20a-5p 23150.6 0.018 267 0.488
NM_001402.5 587 MIMAT0000093 EEF1A1 9041.62 CDS 7758.62 hsa-miR-93-5p 24640.4 0.018 268 0.49
NM_001402.5 587 MIMAT0000680 EEF1A1 9041.62 CDS 7758.62 hsa-miR-106b-5p 26739.4 0.018 270 0.493
NM_001402.5 634 MIMAT0000261 EEF1A1 9041.62 CDS 8758.62 hsa-miR-183-5p 22071.5 0.019 283 0.551
NM_001402.5 697 MIMAT0000457 EEF1A1 9041.62 CDS 8263.62 hsa-miR-188-5p 1933.4 0.071 778 5.516
NM_001402.5 731 MIMAT0026625 EEF1A1 9041.62 CDS 7554.62 hsa-miR-653-3p 13284.5 0.025 350 0.889
NM_001402.5 743 MIMAT0002874 EEF1A1 9041.62 CDS 7554.62 hsa-miR-503-5p 8657.98 0.113 1487 16.822
NM_001402.5 805 MIMAT0000064 EEF1A1 9041.62 CDS 5791.62 hsa-let-7c-5p 2773.81 0.025 290 0.731
NM_001402.5 805 MIMAT0000063 EEF1A1 9041.62 CDS 5791.62 hsa-let-7b-5p 19186.699 0.025 361 0.911
NM_001402.5 805 MIMAT0000096 EEF1A1 9041.62 CDS 5791.62 hsa-miR-98-5p 21951.5 0.025 366 0.923
NM_001402.5 805 MIMAT0000065 EEF1A1 9041.62 CDS 5791.62 hsa-let-7d-5p 22014.4 0.025 366 0.923
NM_001402.5 805 MIMAT0000414 EEF1A1 9041.62 CDS 5791.62 hsa-let-7g-5p 22221.699 0.025 366 0.923
NM_001402.5 805 MIMAT0000415 EEF1A1 9041.62 CDS 5791.62 hsa-let-7i-5p 22400.301 0.025 367 0.926
NM_001402.5 805 MIMAT0000066 EEF1A1 9041.62 CDS 5791.62 hsa-let-7e-5p 23185.301 0.025 368 0.928
NM_001402.5 805 MIMAT0000062 EEF1A1 9041.62 CDS 5791.62 hsa-let-7a-5p 32582.801 0.025 380 0.959
NM_001402.5 805 MIMAT0000067 EEF1A1 9041.62 CDS 5791.62 hsa-let-7f-5p 37968.699 0.025 386 0.974

Cite us

Weill N, Lisi V, Scott N, Dallaire P, Pelloux J, Major F. MirBooking simulates the stoichiometric mode of action of microRNAs, Nucleic Acids Res. 2015 43(14):6730-8.